Unless you’ve been holed up in a cabin in the Siberian outback, it’s been hard to miss the avalanche of research and associated press coverage ballyhooing the connection between microbes and human health and disease in 2013 – and 2014 will be no different, as fecal transplants become the new black!

Name just about any ailment plaguing humanity and you will find some researcher, somewhere, working the microbial angle for a causal or correlative connection. More federal funding please!

But reading between the lines of the near breathless and optimistic reporting on the human microbiome, sits a sobering fact: scientists know very little about the connection between disease and the potential microbial culprits (these are early days). Science is hard and the human gut is a vast and diverse ecosystem. As with any ecosystem, it’s the community as a whole that’s likely more important, not single members per se. Connecting the dots when there are lots of them – and they are shape shifting all the time – is proving to be tough (a similar reality has slowed our understanding of the role of human genes in disease). This will take some time – but the writing is on the wall.

That said, projects like American Gut (think about joining the project!) are trying to map the diversity of the human gut. By sequencing the gut microbes of tens of thousands of regular folks – of all shapes, sizes, and of diverse diet and lifestyles – we hope to see coarse-grained patterns shaped by disease state, age, diet, lifestyle habits, and so on. These broad strokes will then allow researchers from all over the world (yes, de-identified American Gut data is open source and made available to the research community – thanks good folks over at Earth Microbiome Project) to dig a little deeper to see what might matter the most when it comes to maintaining a healthy microbiome at different stages of life (yup, a 2 year old harbors different microbial compositions than grandpa).

In addition to a large sample of westerners, we will also able to compare these tens of thousands of samples to other data sets – including groups from Africa, India, South America, and so on. Excitingly, our work with the Hadzabe hunter-gatherers in Tanzania will allow us to compare our western selves to people who still hunt and gather the majority of their food, have limited access to western medications, are all born naturally and breastfed for 2+ years, live outside more or less 24/7, are covered in microbial-laden soil (natures blanket), and that have an intimate connection to a vast (natural) microbial world that we in the so-called developed world have moved away from. We don’t know what we will learn over the coming years, but it’s a given we will be a little smarter when it comes to modulating and nudging our gut microbes in a healthier direction with diet and lifestyle choices (I sure hate to see Big Pharma drug our microbiome into compliance – lets not let it happen folks!).

As researchers continue to build the scientific case for the microbe-health connection in 2014, I’m embarking on a little self-exploration. On January, 1, 2014, I began the first of many diets that I hope will lead to a better understanding – at least for me – of not only what a healthier gut microbiome might look like in a modern world, but also more importantly, what it shouldn’t look like. I will be collecting daily stool samples along the way for subsequent 16S rRNA analysis throughout the next 365 days.

On Jan 1 I started a high fat-protein diet with very, very little carbohydrates and near zero quantities of dietary fiber. In short, I’m attempting to starve my microbes of much-needed substrates for growth – such as dietary fiber, resistant starch, etc. I’m not arguing that anyone should do this on a regular basis, nor am I suggesting this is a good or bad dietary strategy, but I am trying to whack my microbiome around a bit to demonstrate that significant shifts in your gut microbiota can be achieved in very short periods of time with significant shifts in macronutrients.

I experienced this past summer how dramatically you can shift your gut bugs with diet when I traveled from New Orleans to West Texas where I was held up for a few months trying to finish a book (BLOOM will be out this year!). As I drove out of New Orleans, I left behind a diet heavy on meat, but with a quantity and diversity of dietary fiber that would make Michelle Obama smile. But once I landed in the parched landscape of West Texas near Big Bend National Park, the little writers shack I rented lacked some modern niceties – like a kitchen. So I ate most of my meals at the local watering hole(s). Below is a graph of what happened to my gut microbes.

As the pie charts below reveal, I look like an entirely different person – microbially-speaking. On the left my New Orleans microbiome were dominated by the phyla Firmicutes (74.80%). But after only 2-3 weeks of greatly reduced consumption of dietary fiber – remember, I still ate lots of meat – my Firmicutes dropped to 28.63%, while my Bacteroidetes shot up. In other words, my Firmicutes and Bacteroidetes traded places in my new desert belly.

Digging a little deeper in the data reveals that much of this dramatic shift can be attributed to a handful of genera. The bar graph below shows that my Bacteroides (in the phyla Bacteroidetes) seem to really like my no, to super low plant intake – going from a mere 15.91% relative abundance in New Orleans to a whopping 56.59% in my near plant less desert diet. Consequently, the relative abundance of the Family Ruminococcaceae took a hit along with the Family Lachnospiraceae and the Genus Ruminococcus. These three are known plant fermenters – that is, they metabolize dietary plant polysaccharides – that didn’t seem to compete very well as the fermentable substrates (fiber, resistant starch) dried up.

Also of interest are my Bifidobacterium levels which went from 5.46% in New Orleans, to 0.10% and my levels of Paraprevotella (kissing cousin of Prevotella) went from a paltry 0.40% to a monstrous 7.20% in the desert (red bar spiking on right-hand side of graph). In the case of Bifidobacterium levels taking a hit – note I like Bifidobacterium as they are often cited as being part of a healthy and balanced gut flora – I would go out on a limb and suggest they were suppressed due to my lack onions, garlic, leek etc. Though I suspect I could be wrong – but that’s my hunch at the moment. As for the increase Paraprevotella, I would again go out on a limb and suggest this spike is attributed to my modest intake of whole grains via Muesli-like cereal – essentially eaten dry every morning in my desert home. Something I didn’t do in New Orleans. Anyone that follows this blog knows I have something of a (Para)Prevotella fetish and attribute the increased relative abundance in many/some folks as a sign of “whole” grain consumption, not fiber intake per se as often argued. Strikingly, elevated levels of Prevotella have been noted among HIV-infected individuals who exhibit chronic gut inflammation. In this study, the researchers suggest that Prevotella may thrive under conditions of inflammation. In another study, researchers found that Prevotella strongly correlated with new-onset untreated rheumatoid arthritis. On the flipside, reduced rather than increased levels of Prevotella correlated with kids diagnosed with autism compared to symptom-free neurotypical children in a recent study. However, it’s interesting to note that many families will place ASD kids on a gluten and casein free diet following diagnosis. Therefore, if my “out on a limb” theory that Prevotella levels are associated with whole grain consumption is near the mark, then lower levels of Prevotella in these diagnosed youngsters is not completely unexpected. In other words, in diagnosed ASD kids the lower to no levels of Prevotella may have more to do with diet than the disease state. But we will wait and see how this shakes out over the coming years.

A new coffee-table-like book about our work in Africa will be available soon. Click here if you want to receive an e-mail when the book is available. 100% of the proceeds go to the research.

If you spend anytime reading the literature on Bacteroides – the genus that dominated my desert belly – you will quickly surmise that most researchers attribute it to a high fat western diet. It’s close to dogma. However, in my little New Orleans to desert diet experiment, my levels of meat and thus by extension, fat and protein, stayed more or less the same. The only thing that changed that much was my reduction in plants and the fermentable fibers they contain. So in my Sample Size of One, changes in my intake of meat can’t really explain the striking shifts seen in the graphs above. So rather then Bacteroides thriving in a fat-soaked environment of my desert gut, they likely gained a toehold in my increasing alkaline gut. Like many microbes, many strains of Bacteroides seem to be pH sensitive. And the main driver of the acidity of your colon is fermentation. Reduce the amount of dietary fiber and resistant starch reaching your colon (ie, no plants), the pH rises and becomes more alkaline due to a reduction of short chain fatty acids and other organic acids that are byproducts produced during fermentation. As pH rises, those microbes that are otherwise pH sensitive bloom. So, my “out on a limb” interpretation of the dramatic shift in my microbial community in the example/experiment above is not driven by increased meat consumption, but rather my shift in pH due to the lack of fermentation which ultimately provided fertile ground for Bacteroides to dominate. My increase in the phyla Proteobacteria from 0.03% in New Orleans to 2.63% in the desert, suggests this new, less acidic ecosystem may have favored some opportunistic pathogens. And in one final gut check – and most concerning of all to me, is the overall diversity of my gut microbiota was halved in the desert (as measured by species equivalent OTU’s). And as Ecosystems 101 teaches us, a less diverse microbiota is less resilient to perturbations and may tip one a tad closer to an unhealthy state. One recent study suggests that my reduction in gut microbial diversity – while not dramatically altering my sanitation and hygiene practices in the process – may have had a lot to do with my reduction in dietary fiber. This is also been seen in mice fed high versus low fiber diets (personal communication, Justin Sonnenburg, Stanford University)

My little experiment coupled with a steady flow of papers suggesting diet and lifestyle can dramatically impact your gut microbial composition in short period of time, has led me to my 2014 goal of acquiring and catching the healthiest gut microbiome in the world. By catching, I mean it’s not all about what you eat, but how and where you live – and whom you live with – and your interaction with the microbial world around us.

Throughout 2014 I will undertake a series of dramatic shifts in my diet and lifestyle in attempt to whack my microbiome around. For example, aside from the high fat/protein diet I just finished at the first of the this year (taking poo samples along the way), I will go on a raw food diet for a few weeks, followed by a juicing diet, possibly followed by a vegan diet, followed by an Atkins-like diet, followed by a Mediterranean diet, followed by a period of fasting, possibly a weeks of lots of fermented foods, followed by a Paleo diet, followed by Jenny Craig and Weight Watchers diets, followed by a Master Cleanse Diet, and so forth – repeating some diets several times. I will also go on the occasional drinking binge, exploring the impact of beer, wine and Jose Cuervo on my microbiota. Don’t tell John Boehner, but I will also explore the impact of copious amounts of weed as I wake and bake for a week while holding various diets constant. But perhaps the most interesting will be my hunter gatherer plunge I will take 2-3 times as I live and work among the Hadza hunter gatherers of Tanzania – where I started working in 2013 (Science did a nice 3-pager on our project recently if you want to learn more – see also tiny blurb in Nature). As a newly minted hunter-gatherer I will live in a grass hut, forage for plants and consume wild game (zebra, impala, kudu, baboons, wart hog, birds, etc.) and drink their water, all the while collecting my stool samples. It will be interesting to see if I can shift my western gut – which ever one I have at the time – to look more like the Hadza. I suspect my exposure to the microbes in the Hadza environment will dramatically alter my microbial composition and increase the overall diversity. But will it last when I return home?

I’m not sure what I will learn at this point, but will share my results with colleagues and ask them to weigh in on the microbial compositions generated by the various diets. I will ask them to do so without knowledge of the diet that produced the results in an effort to remove bias against any particular diet/strategy/lifestyle – such as the bias we see over at US News & World Report as they continue to deliver an ass whopping to the Paleo diet every year as they rank the healthiest diets on an annual basis. Will I nail down the diet and lifestyle that results in an optimal microbiome – whatever that is? Don’t know for sure but I’m pretty confident I will learn which diet and lifestyle choices yield less than optimal outcomes for my gut bugs. If anyone out there has any diets – crazy or mainstream – they would like me to consider, ping me. Let the games begin.

You can watch for free on Hulu or Netfix streaming- also from Website – Fat sick nearly dead- hulu link- books you might find interesting – The Story of the Human Body- Evolution, Health, and Disease-Daniel E. Lieberman-Grain Brain- author -PerlMutter. Eating on the Wild Side.
All on Amazon. Would like to know more about Pre-biotics and Epigenetic effects re Flora.

Please do view the film and also check out the ‘nutritarian’ eating style as described by Joel Fuhrman, MD (Eat to Live, Eat for Health, etc.) who was Joe Cross’s physician and appears in the film. Perhaps it is a diet that is high in diverse phytonutrients that supports a healthy gut microbiome.

This is an amazing experiment. Just discovered this site btw, very well thought out posts.

But…as interesting as your experiments sound, you’re missing a balanced long term sustainable diet in your experiments. How to maintain a healthy gut microbiome on that diet is what I think would be most relevant for everyone. This diet includes sweets, beer, “processed” foods, as well as healthy foods. Good luck excited to see the results.

Can you do the Jose Cuervo experiment first? In particular, as a chaser after two tablespoons of potato starch. All kidding aside, THANK YOU for being our guinea pig. I wish I could test at home like I do for blood ketones and glucose. Maybe someday.

Firstly, I just wanted to say I’m following your hard work on your gut microbiota and thank you very much for sharing the information. You are not alone in the points you make against some other researcher, etc, because I think many of your readers trust in the results you share and the points you make are exactly what any knowledgable person in your situation should consider, so, if you have more out on a limb thoughts, please don’t hesitate to share them.
I think something you might like to do may be, instead of following only certain diets, also determining what kinds of other diets you might like to try and trying them.
When it comes to fiber, the best easy source of information I’ve found yet is the 5 part fiber manifesto of Sarah Ballantyne at http://www.thepaleomom.com/?s=fiber
In part 2 the types of fiber are classified as insoluble/soluble and fermentable/nonfermentable and explained further. You may want to create diets of different concentrations of different fibers and try them. Another thing I’d add is not to forget that too much of a good thing may be bad, and it applies to fiber and bacterial overgrowths, I’ve experimented it myself after eating plates of steamed jerusalem artichokes, so keep a limit of fodmaps such as inulin, which is a fructan, other fructans, polyols and foods with a high ratio of fructose/glucose. Something I’ve found out helpful is that pulverizing some fodmap foods greatly lessened the disturbing effects, possibly due to breaking fibers into pieces significantly and therefore giving less of a chance for the overgrown bacterias to feed on them. You may find a good list of fodmaps at http://www.eat-real-food-paleodietitian.com/paleo-diet-and-fodmap.html which I first found at http://www.thepaleomom.com/2012/08/modifying-paleo-for-fodmap-intolerance.html
You may also want to try some supplements that change or may change gut microbiota, such as berberine and Prescript Assist.

Jeff – what role would bacterial genes in the food one eats play for the fecal microbiota analysis? Do you think these genes could add significant noise to the American gut analyses, so as to not be sure of how much of the genes that come from external sources as compared to bacteria actually residing in the gut?

Drink nothing but full fat grass fed raw milk for a week and see what happens. I’d love to see if it does to you what it did to me ( hives upon eating again, high meat and fat diet ) and then if it goes away from your rapid diet change. Then again, it sucked, so I’d hate for it to do that to you as well… The good news is vegan diet fixed it after long term struggling.

Awesome N=1, can’t wait to follow it. I was wondering, and you would be the guy to ask, if you thought that the diversity in the gut is responsible for our metabolic flexibility as well as our ability to adapt to changing seasons. It seems to me that these shifts we see in in meat-based diets could be a way to switch on thriftiness traits that may either slow metabolism or affect nutrient storage. For example, could the inflammation related to a meat-based diet be a mechanism by which you could induce insulin resistance and become more adept at storing bodyfat or better preserve glucose? It seems to make sense that as you shift seasons and plant materials become more scarce, there would be an advantage to being able to shift some of the last remaining carbohydrate intake in to fat deposition for the upcoming “lean” season.

i written about this in a few places. i think the low grade inflammation (endotoxemia) associated with high fat diet (LPS leaking into gut) is an evolutionary strategy to trigger insulin resistance which conserves glucose. you see this among the hadza – when there is lots of meat, carbs drop off a bit.

pretty sure there this wouldn’t yield anything. if it did, not sure how as GMO vs conventional isn’t going to change substrates to the colon and provide anything out the ordinary to the gut bugs. but u nvr know. would need a very well controlled study with a considerable amount of participants.

Will be following this closely. Even if there was little microbial change with GMO and processed foods it would be interesting to see the results anyway. I think this would also appeal to a broad audience.

The process of creating any and all GMOs requires first a vector (pathogenic bacteria or a virus) to enter the target cells with the new DNA, second some DNA for antibiotic resistance attached to the new DNA to be inserted, so the cells with the new DNA can resist the antibiotic selective agent to sort out the ones that didn’t take. So, all GMOs contain pathogenic bacteria (mycoplasma) or viruses, viral or bacterial susceptibility in order to contain the new DNA, and antibiotic resistance to survive the sorting process. Combine that with microbial ability to exchange genetic material in the gut. You would probably end up with a gut full of super bugs resistant to antibiotics but susceptible to viruses which cause evolutionary mutation. (It’s not antibiotics in animal feed causing antibiotic resistance, but antibiotic resistance in human feed.)

Yes, it does. It always has. What I’m saying is that genes transferred from GMOs to our guts have some scary qualities. They have antibiotic resistance built in, so if you do acquire a pathogen in your gut, it can grab the antibiotic resistance gene from your GMO food. Also, commensal viruses and bacteria in our guts can grab pathogenic abilities from the vector DNA in GMOs. When biowarfare scientists were searching nature for antibiotic resistance to include in their bio-potions, they found it in bacillus thurengensis. So, all Bt GMOs can share antibiotic resistance with any microbe they come in contact with. When we eat GMOs, we are brewing antibiotic resistance inside our guts.

Brian / 20 January 2014

Amen Jeff; solid point. Also, ‘Laura’, do any work in genetics? Because I make mutations in bacteria and eukaryotic cells all the time and it does NOT require “pathogenic bacteria or viruses”. Many species are able to transiently take up eDNA, which could have simply been a PCR product of any random gene. In addition, one could easily do ‘Mendelian’-style breeding and come up with almost all of the GMOs that you speak of, it would just take much longer and cost way more. In fact, some companies are attempting to do this right now because people freak out about the title GMO for no reason. Look what ‘conventional’ breeding has done to canines…many breeds die because of traits that owners have purposely selected for. But that must be okay right? Because it was done the old fashion way….

YourMom / 19 January 2014

Jeff, this is a TED talk published June of 2013, Ex-Biotech Scientist Gives TED Talk on the Dangers of GMOs. Interestingly, he specifically speaks of the impact on Gut Bacteria right after the 00:08:00 minute mark.

Thierry Vrain is a former research scientist for Agriculture Canada. He now promotes awareness of the dangers of genetically modified foods.

For most of Thierry Vrain’s career, he supported the cultivation and consumption of GM crops, but in the last 10 years he has changed his position because of the flow of published studies coming from Europe, some from prestigious labs and published in prestigious scientific journals, that questioned the impact and safety of engineered food.

He refutes the claims of the biotechnology companies that their engineered crops yield more, that they require less pesticide applications, that they have no impact on the environment and of course that they are safe to eat.

When the first GMO crops were introduced in the mid-1990′s, they were marketed (and received) as ‘magic’ — a perfectly safe, practically water-like substance that erased pest problems without changing the quality of the food.

In this TED talk given recently to an audience in America, Thierry explains the rising phenomenon of superweeds, genetic pollution, antibiotic resistance and food allergies, all attributable to GMO agriculture.

GMO or not, it is likely higher consumption of pesticides, herbicides, fungicides, etc would have a measurable effect on the gut microbiota as these substances are meant to kill the little critters. Genetic modification itself probably unlikely to measurably impact but higher levels of little critter killing substances in food likely would impact the gut microbiome. It’d be real interesting to study gut bacteria of GMO farmers where the fields are soaked in glyphosate.

Thanks, Jeff, for the incredibly important work you are doing. We’re having a lot of fun with the data you are providing over at Heisenbug HQ. I’m glad to see some confirmation of the Bacteroides/alkaline connection — the idea that they somehow thrive with meat/fat intake, apart from fiber/plant intake, never made much sense to me.

So I take it you think the Proteobacteria bloom is a response to the overall rise in ph, and not a direct response to the drop in Actinobacteria/Bifidobacteria?

Oh, and please feel free to go “out on a limb” more often — it’s the only way to ever figure out anything useful!

good points and yes, i think my drop on actino (didn’t feed them) along with other fermenters greatly reduced SCFAs and thus pH. i “think” this opened the door for some proteo. but not 100% sure. we will see. thx for comments!

i only plotted the top 30 in the bar chart – was getting too hard to read including more. the proteo seem to be (will sort out which strains are likely in a few weeks):
k__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Neisseriales;f__Neisseriaceae;g__Neisseria
k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacteriales;f__Enterobacteriaceae;g__
k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacteriales;f__Enterobacteriaceae;g__Serratia
k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__;g__
k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__mitochondria;g__
k__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Rhodocyclales;f__Rhodocyclaceae;g__
k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalorhabdales;f__;g__
k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__

I agree with you and inflammation/grains/Provotella. What you are talking about is the conclusion I have reach through my own experience. I had been ill 25+ years and found that a paleo diet was a big factor in managing my condition/symptoms so only ate veg and protein, if I had any sugars or carbs then the brain fog, disbyosis, cognitive and fatigue symptoms would sky rocket. I stumbled on this connection when I first tried the Atkins diet. I thought this might have been because I lacked a diversity of gut flora having been on a lot of antibiotics during my life both as a child for a heart murmur and then as an adult for various infections. Then to years ago I under went two weeks of donor stool infusion at the Centre for Digestive Diseases in Sydney – Prof Thomas Borody. He put me on the antibiotic Rifampacin to sterilize the gut, with his permission I incorporated Dr Anju Usmans (Autism Research) biofilm protocl for two months with the antibiotic. At about the 6 week stage of the preparation the weight fell off me, I could never get my weight down before this, if I ate carbs overnight a couple of kilos would go on and this would continue whilst I ate carbs. I then underwent daily donor stool infusion for two weeks. I was glowing with health and vitality, I looked 20 yrs younger and felt incredibly well, like a teenager again. No more leaky gut, no more food intolerances, all my symptoms gone and hence I went back to work . My general Dr congratulated me on these results. However this effect slowly subsided and after about 8 weeks my symptoms crept back in. and my cognitive ability declined so I had to stop work again. So about a year later I did my own donor stool infusions from an approved donor for about 3 weeks. But nil, nothing, zilch, no benefit at all. Then about 12 mths later I found out I had lyme disease. Now on IV abx and again the abx Rifampacin, so I expected the weight to drop of again and the inflammation to go. But no this didn’t happen and it has been 3 months on the abx. So my conclusion is that the diet is the missing peace, I haven’t been eating grains or high fructose fruit but did have berries in my diet. so I decided to eat just meat and veg again, now two weeks into this and I am now again starting to see the fluid/weight come off me well I am pretty sure it is inflammation, just as you mentioned in your post above. My hunch is that 2 months on from now on just meat and veg with the abx all the inflammation will have gone again. I am very interested in your experiences as it directly affects me. Once I have finished with abx I will again undergo donor stool infusion, but realize this is only part of the puzzle, I have to feed the desirable flora so they will establish in my gut and flourish. So I am following you with great interest. Good luck and thank you for your GUTS to be the guinea pig in your research!!!
crusaderD

I was very excited to read about your experiment, and will be following your progress closely. I have been following a diet for the past ~ 16 years that you may be familiar with; the Specific Carbohydrate Diet (SCD). This diet was developed by Dr. Sidney Valentine Haas, a New York City pediatrician and professor of pediatrics, in the 1920’s to treat Celiac’s disease.

The SCD was brought to the public’s attention by Elaine Gottschall when she wrote “Food and the Gut Reaction”, and later, “Breaking the Vicious Cycle; Intestinal Health Through Diet”. In her book she recounts her experience taking her young daughter to a then ~90 year old and still practicin, Dr. Haas in a last ditch attempt to avoid surgical removal of her daughter’s colon due to refractory ulcerative colitis. Her daughter followed the SCD strictly and after 2 years was completely symptom free and has remained so throughout adulthood. Since publication of these books many people around the world have used the SCD to treat both Crohn’s disease and UC, with a lot of anecdotal success. The only officially recognized SCD resources, should you be interested in discovering what the SCD entails, are the book “Breaking the Vicious Cycle; Intestinal Health Through Diet”, by Elaine Gottschall, and the website http://www.breakingtheviciouscycle.info .

We SCDers have organized ourselves into networks that help each other with the implementation of the diet and support each other throughout the healing process. Many of us have been told that “diet has nothing to do with IBD” by our doctors, and have been actively discouraged from following the SCD. This is very galling, since the diet has not been studied, for one thing, is a well-balanced, nutritious diet (IBD patients are often severely undernourished), for another, and lastly, the medical community does not have many good options for treating these diseases and do not know what causes them!

The hypothetical explanation for the efficacy of the diet is that it selectively starves pathogenic bacteria while feeding beneficial bacteria in the gut as well as maximally nourishing the patient. Research needs to be done in this area to either support or disprove this theory. An intriguing fact: this diet has been noticed by the ASD community and is being used very effectively by parents to treat their children on the autism spectrum, (anecdotally of course). These parents report very positive results: why is it helping these children?

Lastly, although US physicians are now prohibited by the FDA from using FMT to treat IBD patients, there is nothing stopping them from advising patients to try FMT or from supporting patients’ own DIY FMT sessions at home with how-to instructions and donor screening. I’m told that some of these patients are being advised to follow the SCD during and after FMT treatments. Many success stories are being shared in FMT networks.

Something is going on here, and it is not a newly discovered phenomenon. THIS DIET NEEDS TO BE STUDIED!!! Please consider adding a trial of strict SCD into your experiment. Thank you for your consideration.

I have been asking my gastroenterologist for a fecal transplant for years. I suspect a fecal pill will be available soon and his services will probably no longer be necessary.

A suggestion for another diet would be the Perfect Health Diet which is basically Paleo with safe starches (potatoes, white rice, etc) and milk. I currently follow this diet although I don’t consume milk products (homemade yogurt and kefir) any longer. I moved to Wisconsin, “America’s Dairy Land”, recently and the backwards state doesn’t allow the sale of raw milk.

Another suggestion would be to follow the Weston A. Price Foundation dietary guidelines.

You might want to try CRON –calorie restriction with optimal nutrition. Such diets are usually very strong on vegetables. Also of interest (perhaps together with CRON) is reduction in protein — this tens to lower IGF1). It would be interesting if the lower calorie food — which has many positive effects in global health — might also have distinctive effects in the gut microbiome.

Very curious to see your results, as the AGP profile showed me to have a huge amount of proteobacteria, which is not associated with normalcy or good health. I had a hospital infection a little over a decade ago, and I imagine my normal flora was wiped out at that time by strong antibiotics. I hope I can repair the system…

Maybe it might be time to explain that high Proteo may not necessarily be a bad thing. We’re looking at best Genus, and sometimes Family designations here (not the fault of research, just current abilities based on cash, time, molecular genetics and sequencing platforms). I’ve worked with and there are many well known instances of species being ‘mis-classified’, subspecies that really don’t exist and MAJOR strain-based differences WITHIN a given species (I’ve got a bug that differs up to 12% within the genomes of just 5 sequenced strains). I haven’t been (very) sick/taken antibiotics in over 5 years and I had/have 30% Proteo as of last month with my AGP output. To note why I don’t think it’s always a bad thing… I am doing my PhD in Microbiology (so it hasn’t caused ‘brain fog’ otherwise I wouldn’t have made the cut) and have managed to row and/or run to medal podiums in on-water races, 6 marathons, 6 half-marathons, and various shorter distances. Also, BMI of 22, BF of 8%, RHR of 38. Try thinking about Escherichia coli Nissle 1917 versus EHEC or EPEC!

I think you make a good point — phyla classification can only tell us so much when even strains can differ greatly (like your example of E. coli Nissle 1917).

But to provide a counterpoint: we can still tell a lot from correlations. Every study I’ve ever seen that attempts to tease out the connection between microbiota and disease by looking at phyla-level fluctuations has Proteobacteria ALWAYS positively correlated to worse disease profiles. In other words, if you see Proteobacteria rise, it never seems to mean good things. And vice versa. I would love to see a study that showed something different, but I have yet to see it.

Point taken Sir. Just saying, I work with multiple gastro-instestinal tract species every day, help to set up clinical trials and do genetics/genomics work, so I see 1) how ‘pathogen’ is frequently niche-specific, whether that niche is physical in the host or potentially the host’s specific immunological state 2) that clinical study enrollment/design can have many flaws (not enough people to do power analyses or simply taking white females…ect.). Frequently when people see high Proteo in studies I believe it’s a almost complete replacement of everything else, very transient also; yet as for myself, I still have 40% Bacteroides and 20% Firmi. The great part about this work at AGP is that it will give a large swath of data to look through. But when people quote books or blogs by people who are non-scientists or do not do their own research it does scare me a bit. A potential purpose of this study seems to ‘debunk’ (neither good nor bad way) what the ‘normal’ flora has been found to be so far by adding in many more samples (as well as potentially confounding variables). I think the study is a great project, but the idea that ‘1 diet does this’ or ‘1 species does that’ is going to vary so greatly across a population. General correlations will probably hold true and be good, but look at any one given person and there will probably be high variance. Just think of why we need to have so many replicates in animal experiments; it’s not because we love working with massive colonies of mice!

couldn’t agree more. the AGP is yielding some interesting correlations. but we will see how this looks at 20,000 participants. we will be out putting some additional study-wide results in the nxt month or so. as for my DIY, almost everyone working with the gut microbiome has sequenced their own poo – i’m just taking a bit further. as for debunk, not my goal. just curious for my own reasons…and yes, sample size of 1 is limiting, as i indicate. preaching to the choir on that one…

would be interesting to know what strains u have in your proteo. hard to know if its a good or bad thing unless u know who’s in there. big diff between a cat (kitty) on your kitchen counter or a CAT (as in big cat).

Jeff, good points and need to reiterate that I love the study! ‘Debunk’ was a bad usage of the word, and I didn’t quite mean that. You’re building on very solid previous work done by labs such as Relman, Gordon, Turnbaugh, Fishbach, Goodman, and Gilbert (mainly gut but obviously others have done oral, nasopharengeal and skin). But previous sample sizes, restrictions to studying specific diseases/populations and such have probably hampered microbiome research in general.

Jeff, I think we all probably agree more than we disagree. But I wanted to make one more point: the value of looking at correlations is in phlyum-level fluctuation, not species composition. In other words, if you have done something to make your microbiome more hospitable to Proteobacteria, I do believe that’s relevant — isn’t alkaliphilia a phylum-wide characteristic of Proteobacteria, regardless of species? In other words, ok, we can hope that it’s all E. coli Nissle 1917 in there, but even if it is, have we not swung the door wide open to any and all Proteo? Has that kind of fluctuation ever shown to be a good thing? And that’s why correlations are so uniformly negative in this regard and probably shouldn’t be so easily ignored.

Maureen, this experiment WAS a low FODMAP diet. Very low carb, no plant fiber. These are the results of a low FODMAP diet. No surprise: it’s a diet designed to stimulate little to no fermentation in the gut.

The only exception might be lactose — I don’t know if Jeff consumed milk or not. But lactose is optional on a low FODMAP diet anyway.

I hope you take samples of the water you are drinking and bathing in as well – and record anything you put in your mouth, even toothpaste, herbs, NSAIDS, etc. or on your skin.
I am curious if all the flora in the gut microbiome have been identified and what your global experiment will find.
Since in the past scientists have reached for conclusions too hurriedly it would be good to avoid that tendency. Haste makes waste.
I wonder if Ayurveda or TCM or even diets like the Blood Type diet (which I have felt doubtful about but which people report success with) might be meaningful to consider as dimensions for your analysis – if you are consuming foods that are basically not agreeable to your constitutional type it probably can’t be that good for your gut.
Best wishes! – this will be very interesting to follow.

I can’t wait to hear which diet leaves you with the best, most diverse mix of gut microbes. Be sure to keep us all informed along the way so we can improve our guts, too. Thanks for being the guinea pig Jeff. You rock.

How about the Specific Carbohydrate Diet, I use it to control my Crohns medication free. (Basically gluten (all grains really) lactose, starch, sugar free) I have experimented with my gut for the past 6 years trying to find the right food balance to stay med free. I would say I am working in the blind since I don’t get to sample, rather I pay close attention to what my body tells me about the food I eat. Processed food is the devil for me. I have also travelled a lot and noted the differences in food quality are huge. (Example 10 weeks in Romania on all local cuisine had me feeling great and eating most anything, meat heavy but a lot of veggies I do not normally eat, but I have added to my diet now) Back in a tropical climate (HI) now is a bit more difficult, of course each climate has also seen marked lifestyle changes … activity and exercise matter a lot.
Just some of my own observations in the fight to make my gut bugs happy.
Can’t wait to see the results of your journey.

Could you try a low-carb-high-fat (LCHF) diet? LCHF includes an adequate protein (say ~20% of total calories) intake. This could include many vegetables with fiber slathered in butter, olive oil, or ghee.

Awesome experiment. Any chance you be taking blood samples for glucose levels, cholesterol inflammation indicators, etc. Also will you be testing insulin sensitivity and possible changes to sleep habits?

I’m gonna second JMD’s suggestion and say you should try SCD! I’ve been on it for 5 months to treat Crohn’s disease and I have seen better progress in the last 5 months than the last 3 years on prescription drugs.

Fascinating stuff. I’d love to see you try the GAPS Intro diet. It’s specifically designed to heal “leaky gut” and rebalance the gut flora. Would be interesting to see its impact. It’s based on this book by Dr. Natasha Campbell-McBride: http://amzn.com/0954852028

Have you heard of Plexus? I have been told by more than a few people that taking it while not changing any other aspect of one’s diet can alter your gut chemistry enough to resolve insulin resistance, chronic yeast problems, resolves all sorts of GI issues, etc. It is also supposed to improve weight loss. I haven’t started taking it but am contemplating. I have PCOS (Poly-cystic Ovarian Syndrome) and am trying to get it under control, along with all the issues that come up because of it.

My son is on the autism spectrum and has the homozygous MTHFR genetic mutation for A1298C affecting methylfolate/folate metabolism. It would be quite intriguing to look at interactions between folate metabolism and gut bacteria especially since the study mentioned comparing autistic symptoms with Prevotella levels and diet found diet to be largely unrelated. In other words, what about folate metabolism interacts with the gut microbiome?

I read your higher grain consumption as higher gluten and MYCOTOXIN consumption(grains are usually contaminated with toxic mycotoxins from molds) that would’ve caused you gut inflammation resulting in higher undesirable provatella and lower desirable bifidobacteria bugs. Please don’t forget to think about toxic mold mycotoxins that are usually present in all grains and particularly corn. Also, over 90% of coffee is contaminated with mycotoxins as typically are blackened or fermented fruits and veggies. I think that much of the Hadza food is likely contaminated with mycotoxins. Yikes!

Jeff, really looking forward to your research. I would put in another vote for the WAPF dietary guidelines. I would especially be interested in seeing the different between refined grains vs. whole grains vs. fermented/sprouted whole grains. Traditional societies almost always fermented or sprouted grains so it would be helpful to see the different that makes in the gut microbiome. Many people might not be able to tolerate grains now because of the way that they are processed instead of grains being inherently problematic (as argued by Paleo/Primal folks). http://www.westonaprice.org/basics/dietary-guidelines

Angela,
My daughter follows WAPF diet and all her children have become sensitive to grains, even though she is using ancient grains, Spelt, Kamut etc. and soaking them or sprouting them. The youngest (2yrs.) was covered in hives for 3 weeks. He slowly got better after she quit feeding him grains. Also he can’t drink even raw cow’s milk. It may have something to do with poor microbiome development which is seen in the young current generation. Sally Fallon says that people can eat properly prepared grains if a person has healthy gut flora, but something is happening too the gut flora of Western children born today.

Also please try a generalised paleo autoimmune protocol which excludes grains, legumes, dairy maybe except ghee, nightshades and egg whites and puts limits on omega6/omega3[or maybe better, linoleic acid/(Total Omega 3 – alpha-linolenic acid)] ratio and total fructose consumption(better including the half of sucrose, which is also fructose).
This may be out on a limb but maybe gamma-linolenic acid may also change microbiota as omega 3 intake is suggested to effect the microbiota, so you may try capsulated(because it goes rancid quickly) evening primrose oil, or freshly ground hemp seeds for GLA.

If you could do a progression from the gluten/casein free. then to SCD, then to GAPS. We are usually told to try these diets with our autistic children; very curious when you do them back to back how things change. You are super awesome for doing this–very much appreciated!

Very interesting!
Your invitation to recommend or suggest some crazy diet made me think about this dude who calls himself Durianrider, and his girlfriend Freelee. They adovcate one should eat at least 30 bananas a day … You may have heard of them. I don’t recommend you do it as well but anyway, I thought it should be mentioned

I’m wondering what does this all mean? Is it healthier to have more Firmicutes than Bacteroidetes or visa-versa? I’m guessing it’s just diversity we’re looking for. Any clues what all these different microbes “do” for the body? Would love to see an article discussing the health aspect of these findings. Apologies if there is one and I missed it. Or more likely, no one knows for certain.

It’ll be interesting to see how you define paleo when you get to that phase of the testing. Will it be higher carb full of starchy veggies and tubers or more similar to your low carb, high fat and protein diet? Will it have bone broths and ferments?

Also, have you consider experimenting with resistant starch supplementation?

Good luck on your undertaking; looking forward to the results!!! Just a thought re: “Strikingly, elevated levels of Prevotella have been noted among HIV-infected individuals who exhibit chronic gut inflammation. In this study, the researchers suggest that Prevotella may thrive under conditions of inflammation. In another study, researchers found that Prevotella strongly correlated with new-onset untreated rheumatoid arthritis. On the flipside, reduced rather increased levels of Prevotella correlated with kids diagnosed with autism compared to symptom-free neurotypical children in a recent study. However, it’s interesting to note that many families will place ASD kids on a gluten and casein free diet following diagnosis. Therefore, if my “out on a limb” theory that Prevotella levels are associated with whole grain consumption is near the mark, then lower levels of Prevotella in these diagnosed youngsters is not completely unexpected. In other words, in diagnosed ASD kids the lower to no levels of Prevotella may have more to do with diet than the disease state.” Here is my “out on a limb” theory: what if higher levels of Prevotella are similar to a fever – i.e. they are a body’s effort to bring the pathogen/inflammation down? If this is the case, then lower levels of Prevotella in kids with autism maybe a sign that their body/immune system fails to react in an appropriate way to all the inflammation. I think this is a more plausible explanation, as gluten-free diet does not equal no grain diet, and the majority of kids with autism are never placed on any type of diet at all (just drawing on what I see in our schools; usually my son is the only one or one of two kids in a class on a gfcf diet), most people know nothing about diets unfortunately. In addition, disrupted immune response such as lack of fevers is a very frequent occurrence in kids on the spectrum. I’m curious what you think.
Good luck on your journey(s) and please post frequent updates!!!

This is a wonderful thing you are doing. Have you considered checking and reporting on lab results such as A1C and lipid profile? Might have to stay on each diet longer to be fair. The other thing I would be interested in is what you actually ate – like a menu diary. You said you ate dry cereal every day – do you think that eating sprouted bread or sour dough bread instead would have made any difference? As in, is it the gluten or the wheat protein that is bothering so many of us? Or the unaltered phytic acid? What amount of plant intake, what kind of plants and how were they prepared. Was your animal protein often beef or more often fish? What if you just ate raw fish ( so the protein and enzymes wouldn’t be altered) such as pickled herring? And what is your blood type? I will be watching for your next episode. Thank you so much. All the best. Can’t wait for your book.

Jeff, thank you so much for your research, this could be the single most important medical discovery of the century. Some thoughts and questions:
1. Try a raw meat, or all meat diet ala the Inuits.
2. Try the diets or live in the regions with the most centenarians: Okinawa, Sardinia, and in America: the 7th day Adventists.
3. Try adding large amounts of capsuled probiotics like bifido or acidophilous, and see if they actually change the gut bacteria vs. what fermented foods do.

I have a question regarding gut bacteria and kidney stones. There is some research showing certain bacteria ( Oxalobacter formigenes and Lactobacillus and Bifidobacterium) produce enzymes that help digest oxalates and prevent them from entering the blood and then the kidneys. It begs the question if some people are missing the right bacteria, and this is a main contributor to re-occuring kidney stones. Any info or work on that would be helpful to many of us with that very painful disease. Thanks again, and bon voyage!

Jeff, I’m with JT on this one…try the Primal Diet a la Aajonus Vonderplanitz – raw everything, including meat, eggs & dairy. I’ve been doing it myself for nearly a year with awesome results – even my eyesight has improved. If you consult his books you’ll discover his premise that ALL micro-organisms are “good” for us, which is what would make the Primal Diet such a fascinating addition to your poo studies. He taught that bacteria are our bodies ‘janitors’ & went so far as to eat rotted, or “high” meat in order to replenish his bacterial load (this is also described in Weston Price’s observation of the Inuit culture). Aajonus was a controversial dude, but brilliant in his own way. Let me know if you have questions. Have so much fun on your adventure!!

This would such a great addition to your experiment. Aajonus taught that the germ theory of disease is incorrect. He believed that ALL bacteria, fungi, viruses, & parasites serve a purpose in the body: to consume diseased/damaged body tissue. Vomiting/diarrhea are the result of the microorganisms performing their job/detoxification. There is a system to it, you may need guidance – I’m going to suggest my friend Noah Hittner join the conversation – he just wrote an article on Primal Dieting for pt on the net.

Aajonus was unconventional, but his ideas can be liberating – lose the fear of your natural environment, live symbiotically with ALL microorganisms, not just “good bacteria”, because that is truly what our ancestors did. They did not sterilize, pasteurize & overuse antibiotics & then selectively reintroduce a handful of happy ones. IMO that is the newest form of dietary ‘fortification’.

Jeff, I think you’ll be fascinated by his ideas, even if you don’t agree. Again, best of luck to ya 😉

Raw meat, fish, seafood, and raw everything else paleo has been the basis of my raw paleo diet for three years. It deserves its place as the authentic hunter-gatherer diet of the early paleolithic – before mastery of fire, before milk from domesticated animals, and before the use of cooking vessels. Humankind did most of its evolving on this type of diet.

I would like to see the diet principles of Ray Peat PhD followed. It is a low fiber/low polyunsaturated fat diet meant to lower endotoxins and estrogens, and increase thyroid and metabolism. Milk, cheese, beef and lamb, orange juice, cherries, grapes, melons, refined sugar, shellfish, liver.

A very grateful thank you for your pursuit of these projects – both your one-year challenge and the AGP. Getting my initial results from AGP led to interesting conversation with my Dr, who mainly works with ASD kids.
Although not very ‘scientific’, please feel free to expound on your ‘out on a limb’ thoughts. They provide great food for thought. Also, you should talk a bit about what you experience physically, mentally, emotionally with the changes in diet. Sure it is only anecdotal, but that is the underpinning for where most of good research starts.
Keep up the great work !

“talk a bit about what you experience physically, mentally, emotionally with the changes in diet.”
Here’s an idea for making that easy & quick:
before switching to a new diet, answer the question: How old do I feel when I wake up in the morning?

Hi Jeff,
Your chart has made me very curious. I’m a lifelong consumer of vegetables and fruits, and, in the past 3-4 years, my diet has evolved from Paleo to PHD/ancestral.
In addition, I’m healthy and consume some fermented foods, but my gut bacteriome test result shows no traces of Bifidobacterium!
So, can you speculate how one consume plant fibres and resistant starch, but have no Actinobacteria?

The comment thread contains some interesting suggestions for diets, but most are not connected to “how and where you live.” Here’s one that is: Try living on and eating from a diversified farm, one that relies on compost from pastured animals to provide farm fertility & grow produce. Take part in collecting eggs, milking pasture-fed dairy animals, building/turning compost piles, working with veggies, fermenting foods (veggies, dairy, grains, etc.), and/or butchering meat, among other things.

It so happens that my husband & I could offer such an experience in the name of exploratory science. (Though we can’t promise milk in 2014; not yet sure about the pregnancy status of the goats.) The small professional farm that we run is dedicated to producing delicious food in an ecologically diverse setting. Seasonality is a big deal here, thus adding interest and complexity. Let us know if remotely interested. This could be a good quiet place to do some writing, too, as we can offer a private room & bath.

I find your quest so interesting! I have been on a lot of diets in the past couple of years trying to see if I could cure my ailing gut. I tried gluten-casein free, sugar free, Candida diet, GAPS diet, 80-10-10 raw vegan, low oxalate and maybe one or two others. None of them helped long term. Then I read Donna Pessins, Unique Healing. I found her theory of gut bacterial health fascinating and decided to try it out. 2 1/2 months into her program and I am eating things I thought I would never eat again (wheat in the form or sourdough, oats, beans, tons of fruit, honey – it’s been a bit of heaven). Anyhow, hopefully the results last and I continue to heal in the coming months. Her program is supposed to take a year or so but I would highly recommend her book before you being your diet journey. It was quite the “food for thought” about gut health.

So I guess I would recommend her book and adding bentonite clay into your regimen for experiment. Clay has a rich history in the diet of indigenous people and is said to help balance the gut bacteria as well as rid the body of toxins.

Fascinating study and look forward to the results. I’m curious about how you arrived at the order in which these experiments are to be done and the timeframe which each is to be given. There’s one variable that I was wondering if you were considering: nutrient lockout. I know from my former days as a hyrdophonic gardener that unless you start things at the proper ph, a deficiency of just one nutrient can grow into a systemic catastrophe with lockout. I’m wondering if you’ve considered how your data might be skewed by this?

No particular order other than I will return to my typical diet before starting a new one. So what is proper pH? It changes dramatically from one end of the GI tract to the other. Of interest is the colon – which changes proximal to distal, which is all impacted by substrates entering the colon. Not the pH of a food or drink has no impact on colonic pH –

Hi Jeff, I work for Vice magazine and I’d really like to get in touch with you for a short interview for a piece I hope to write about your work. If you’re in Tanzania with the Hadza this will obviously be impossible, but if you’re still in Western society I’d love it if you could get back to me on georgia.bronte@vice.com
Thanks!
G

Very interesting article, thanks. Have you ever heard of the Primal Diet (Aajonus Vonderplanitz)? It’s a raw diet that really opened my eyes to the importance of using friendly microbes for gut health. Mainly, the diet stresses the importance of raw foods (including raw dairy), but it’s different than most other diets in the aspect that it also promotes the healthful aspects of raw meats. The author spent a considerable amount of time with Native American Communities, and even dared eating a fermented meat dish prepared by the Inuit Community (something I wouldn’t do, but he survived, and is convinced his gut flora is stronger because of it, among many other things he’s done). I would be interested in seeing if this diet could be compared to the other diets you are considering. Personally, although I was hesitant in trying this diet, it’s been the best choice of my life so far. Food for thought…if you have time to reply, I’d appreciate your input on this. Best wishes for your research!

Jeff this is so exciting! You are the Neil Armstrong of Gut Exploration! This is one small poop for man, one giant plop for mankind!

I don’t know if this one has been mentioned already but I would like to see effects of the Japanese Village Diet. Something that mimics the Okinawan diet. There is a high percentage of centenarians in Okinawa, They are one of the longest living people in the world. Their diet consists of lots of seafood, sea vegetables, sweet potato, white rice, bitter melon, some unpasteurized traditionally fermented soy products like natto, miso, and soy sauce, etc. and the odd pig from snout to tail and everything in between.

I like the Hadza trip because you are matching the diet with environment and lifestyle. The other diets you will attempt sound interesting but it sounds like you would get much more useful information by travelling to various regions, living and interacting with the people and matching diet with their traditional dishes. You could do this in various regions around the world like India, China, Peru, etc.

For comparison, it would be interesting to live with the Hadza for a period but eat a standard American diet. This way you might be able to distinguish between lifestyle/environmental and dietary factors.

What about testing the effect of behaviors on gut flora? The effects of “hyper-hygiene” like constantly hand sanitizing, bleaching and wearing face masks vs “low-hygiene” not using soap, rarely showering, touching lots of icky things, etc.

would be great to travel to various areas and try their diets in context, but crazy expensive. but to your point, i think the environment is a key piece – something we hope to show with the Hadza… as for the current 2014 strategy of whacking my gut microbiome around, we stick mostly to shofts associated with diets i can follow at home so to speak…. thx for the kind words… and the “plop for mankind” quote…

I just read the transcript for your interview with Chris Kresser. You mentioned that you would eat leeks, onions, and garlic if you were stranded on an island. You talked about the benefits of garlic on the gut. What is it about leeks and onions that is helpful to the gut? Are there any other foods you would recommend as helpful prebiotics? I know that you said lentils were good too which is great because I enjoy eating them!

The reason I am asking is because I am looking to repair my gut because I was on a 1-month stint of Accutane in high school and get a yeast infection after 2 weeks. It went away after I stopped but I suspect that the constant malaise and low-energy that I have been experiencing in the past few years can be attributed to that anti-biotic stint. So any suggestions would be appreciated!

I find myself more and more wondering about the impact of required sanitizers in commercial kitchens and the residue that’s left on the pots, pans, dishes, etc. I own a natural foods store and so many of my customer have had or have developed gut problems over the past five years it seems it must be more than just diet and lifestyle. Really looking forward to following your results this year…

This is such an amazing project! I’ve been doing all sorts of biohacks recently to alter my microbiome, resistant starch, soil based organism probitoics, inulin, and importantly fermented foods like Sauerkraut, Kimchi, etc. I only wish I had had the chance to do this test already so I had a before and after!

+1 on the high meat suggestion. There are many references to it in older literature. And stories of superhuman endurance feats performed after consuming high meat. Lots of online links about making your own. I’d love to know what’s behind it.

I’m not sure to be honest. I’m able to consume Resistant Starch now (in the form of raw green plantains) but I’m not sure if I would have been able to before the FMT, I never tried it. I definitely still have problems – can’t eat digestible starch or FODMAPs without joint / skin / anxiety issues. It may have helped somewhat. Sorry for the unclear answer

Jeff. Hope your heroic 2014 is coming along nicely. Remind me how we can all follow along with the results as they come in. Eager to keep pointing our readers in the right direction. For now, you’re “Best of” in our book:

Jeff, wonderful work. I recently read an article on the theme of “eat to boost good bacterial, and avoid foods that promote bad bacteria” where Dr. Oz cites research from Australia’s Monash University regarding rapidly fermentable sugars (RFS). Oz draws the conclusion from the research that you should avoid: Garlic, onion, leeks, cabbage, cauliflower, mushrooms, asparagus, broccoli, and more. I found what appears to be the source he is referencing and link to it here. I find it contrary to positive things I have seen on your site re: garlic, onion, unless I misread or didn’t get the whole picture. Any thoughts? For quicker viewing you can scroll to bottom it lists the FODMAPs check list http://www.todaysdietitian.com/newarchives/072710p30.shtml

Note it is focused on IBS, but I do not have that and am focused on your general insight into it, would you think, if out on a limb, that the same “cautions” be warranted for health guts (non IBS?)

If nothing else, perhaps its a good food list style diet to experiment with in your year of experimentation to see what happens.

i am curious if you observed the hadza using any form of dental hygiene. frayed ends of sticks rubbing teeth. charcoal, ashes, rubbing on teeth? i know it does directly connect to gut micro biota but if they don’t at all i wonder if there is a connection to dental carries and what percentage was there.

Love your experiment Jeff! Please let me know if you’d like some help with the reagents/kits- I can send you eg some next gen kits that we developed for isolation of DNA from stool. Good luck! Sasha. email: sasha.vlassov@thermofisher.com

This is fantastic! I can’t wait to see the results. Could you consider the McDougall Program it is a modified Vegan – low fat. https://www.drmcdougall.com People with MS and other autoimmune diseases have had some great results on this diet. My guess is that changes to the gut are helping. It’d be great to understand what the diet does to the gut bacteria.

Hi Jeff, it’s me that recommended trying Prescript Assist and I’m very selective but this page concerned me a little, so I thought I should share this with you too:http://fixyourgut.com/hso-probiotics-part-3-prescript-assist/
I’m not sure if those hso’s don’t have existent interaction as I also saw a paper about the bacterias in prescipt assist being present on common foods but opportunistic HSO’s part and especially pseudomonas fluorescens seemed somewhat annoying.
I also wonder what you or others visiting here may think about this as I’m not much knowledgable about it.

Diets to try: Ketogenic Diet. Just completed reading the Wahls Protocol. She describes three diets, the first two would be similar to Low Glycemic/high vegetable, and Paleo/high vegetable. The last one is a ketogenic high vegetable, mostly coconut oil for fat diet.

I love your project!! Thank you! My boyfriend and I have recently dropped as much of ALL starch out of our diet as possible, based on recent research by Dr. Ebringer that suggests a strong relationship between Ankylosing Spondylitis and Klebsiella pneumoniae. Apparently quite a few AS sufferers are halting the progression of their condition by eating this way. It has been fascinating to observe the changes weve been going through. Good luck! We will be following your blog with tremendous interest.

Karin, do you have AS? I have Reactive Arthritis, the “first cousin” of AS and I’ve been troubleshooting with different diets for about 18 months now (completely in remission after 5 months of being in a wheelchair) and would be interested to talk to you.

Cavemanzen, my boyfriend is the one with AS. I am a bodyworker/alternative healing practitioner. I’ve been keeping him mobile for 10 years…. barely. The AS diagnosis and the Ebringer research shed a LOT of light on what has gone on with his body… and I’m feeling like we finally have a chance of reversing this thing! Please feel free to message me privately at FB or planetshpr@aol.com. I would be very interested to hear how you got your arthritis to go into remission and to share info with you that we’ve learned.

You mention that your Prevotella was up in the desert and that it could do with grain intake. I also saw that someone mentioned trying a gluten free diet. You had stated that would be covered in the Paleo diet. Have you tried a diet that is strictly gluten free however pseudo grains such as quinoa, amaranth and teff are consumed and if so did that have the same effect as gluten grains?

My 20 year old daughter and I started on The Microbiome Diet because my daughter has always had bloating, a finicky stomach, etc. This is a gut bug diet. While I know research is still out on what you need to have in your system for optimal health, after reading the book, I could not see how it could hurt. The first three weeks of the diet focus on removing possible problem foods, such as cow’s milk products, grains, starches, and chemicals. Smoothies make up my morning meal, although you could make fruit salads, fruit and nuts (no peanuts), my lunches often include salads rich in garlic, onion, radishes, jicama, spinach, kale and tomatoes, and with a homemade vinagrette. Dinners include a lot of soups and stews with beef, chicken and fish (preferably hormone, mercury, and antibiotic free). Turnips, parsnips and carrots are popular items in the stews and soups. Fermented foods like sauerkraut and kimchi are encouraged, as is coconut oil and olive oil. The idea is to rebalance the gut microbiome so that you are getting maximum nutritional extraction from the foods you eat. Tumeric, tarragon, cinnamon, and ginger are used frequently.

Since we started this two weeks ago, I have lost 7 pounds and my daughter has lost 4, both of us no longer have an extended stomach, and I no longer hear my knees pop when I walk up the stairs. I am sleeping better, I wake up without a lot of grogginess, and I have more energy. I don’t get those energy crashes around 3pm that I used to. I have always loved veggies and fruits, but I also love fried chicken, pastries and bread. It was an adjustment to skip “go-to” foods like bread and cheese. I am 51 and perimenopausal, so I have lots of issues I deal with, and this has helped so far. Interestingly, there is no counting calories in the diet, and I eat until I am satisfied. However, I recorded a day’s worth of foods on Fitness Pal to see what my actual intake was, and it was lower than I expected it to be.

Next week, we will start on the 2nd phase, which introduces cheeses and dairy back in (sheep or goat, preferably), yogurt and kefir, grains like rice and quinoa, and some starchy foods. At this point, the idea is that you have made significant changes in your microbiome and it can handle the newly introduced items better. If you see that you are responding poorly, you know that one of these foods is probably the culprit.

The final phase will be maintenance, and the assumption is that if you follow the diet most of the time (70% or more), you can occasionally splurge and have a little of the things you enjoy most and miss.

My attempt is not scientific in the least, but I am observing how my body is reacting to the changes. My stools have changed a lot, I urinate more, my dreams are more vivid (not sure why that is), and I have less gas (after the first couple of days). My nails are growing faster, and my skin looks brighter. It has not helped or hurt my seasonal allergies so far, which are minor and are more itchy eyes and a bit of stuffy nose, mostly. My biggest change is the level of energy and the lack of aches and pains from being older and over weight.

I love the work you do and love that you’re going to try all these diets. I just love that you’ve even going live off the land in Tanzania!

I’d love to also see an organic vs non-organic produce diet compared as well as one with grass-fed meat vs conventional meat.

I would love to think that we could find one ideal way of eating for everyone but there are so many other factors that come into play and I think we’ll have to figure out the ideal diet for our biochemistry at a particular point in time in our lives. For example: do you have heavy metal toxicity? do you have an candida overgrowth? do you have small intestinal bacterial overgrowth? do you have an autoimmune disease? do you chew your food well? do you eat on the run or sit down and eat slowly? are you stressed with high cortisol? are you going through menopause? what was your mother’s diet like?

I work with anxious women and the gut flora plays such a big role in good mood! Your work is so valuable and I can’t wait to see your results and look forward to your new book!

What a very exciting and timely experiment! Can you share how you are investigating your feces samples? It is funny that I just found this site as I have been reading about commensal bacteria and links to autoimmunity as I embark on a quest to improve my own and my son’s autoimmunity. As a functional nutritionist, I have a firm belief that the foods we eat and assimilate (according to our own unique physiology) play a key role in gut health and the development of disease. I wonder about the probiotic craze and its impact on disease states. It seems to make a huge difference in a lot of disorders, but wonder about possible negative affects in certain individuals predisposed to autoimmunity. Do you have any comments about this? I haven’t fully explored this site yet, perhaps it is discussed somewhere in one of your blogs.

I’m wondering if you are going to try Dr. D’Adamo’s Eat for Your Blood type diet. If you don’t, would you consider telling us what your blood type is when you write up your final reports? Some people have found it relevant and I am curious.

I have many questions about soap and dairy and breastmilk:
Firstly: What microbes exist in breast milk. It is from the lymphatic system, which should be teeming with good bugs. Which ones?
Second: Early Celtic societies used soap bce500. I was raised with lots of dirt and it didn’t save my gut flora from devastation of antibiotics. Detergent started to be used in the 1960’s, as did pesticides. Before that everybody used soap flakes to wash hair, dishes and clothes…Is this where the recent rise in autoimmune disease comes from?
Third: Fermented milk products. The Celtic societies were using milk and fermenting milk. The first use of domesticated animals was milk production in neolithic times. The original shift in gut flora came about a long time ago. Was the co-evolution of bugs and their humans successful in the sense that they remained healthy and thrived on the extra protein?

I was thinking of trying a upper GI biome reboot using breastmilk probiotics but I can’t find enough info about what constitutes healthy bacteria in breast milk, or even what the bacterial makeup was of a healthy woman who had healthy children. I do know recent studies indicate that the bacteria actually travel from the bowels to the breast and speculation that the body may facilitate the transfer. If I find any information, I will be sure to let the world know. In the meantime, if you find any info about where I can find the same info you’re looking for, please let me know.

Something may very well not have been wrong with your breastmilk or its flora, but with your own gut flora to begin with 😉 You pass this on to your children and it’s of the utmost importance for even the second wave of (breast) bacteria to stay alive in their immature guts…

As a gut flora therapist, I see a lot of breastfed children who don’t have optimal intestinal florae, because their mothers and grandmothers didn’t either. They just got set up for failure because of the changed food, medicine and stress environments they were in.

However, breastfeeding of course still is the best choice, for in an already impaired gut, bottle milk will bring further imbalances.

I guess that is what I meant to say. But of course the flora is transmitted through the breastmilk. We were told long ago that it was the vaginal canal that transmitted flora. Now they know the breastmilk itself contains flora.

Thank you for exploring this, would do it myself if I could afford the testing. Have you had any negative or positive long term effects that you can report on yet? When will you do a part 2 post to update us?

I had my own experience with gut bacteria: Fusobacterium varium. Actually it was my significant other, but it affected me too, and it seems to have been the reason for her Ulcerative Colitis which held us in its grip for 10 long and difficult years. Until we, totally accidentally, found a solution to UC which has kept her symptom free for last 11 months so far.

I spent US$ 350 to translate our story (which I authored in German language) into English, so that I can hopefully spare as many people as possible the hard times we had to go through. Whoever is interested in reading because they are directly or indirectly affected, this might be your way out of misery:

I’m a freshwater ecologist and many of my colleagues and I spend a lot of time snorkeling in rivers and creeks that aren’t exactly the most pristine. At conferences there is often mention of someone coming down with a weird illness, high rates of autoimmune diseases and GI aliments. Though this is all anecdotal evidence, I think there is something to be said about the nature of our work and our bodies’ microbiomes possibly being out of whack. It would be interesting to see if some of my colleagues symptoms would improve with a diet/gut microbe make over.

I’m also an avid home brewer. It is well known in the home brewing and home fermentation communities that you can ferment wine, ciders etc. with the natural bacteria and yeast that occurs on the fruit. Depending on the location and season that the fruit was grown you can get a vastly different flavors due to the differences in microbial communities. In reference to traditional diets and changes from region to region culture to culture people are not only getting different microbes, but maybe they are getting the microbial communities appropriate for their diet and microbes that have co-evolved to breakdown the foods that they eat. Eat dirty I guess just like hunter gathers did, pick it off a tree or pick it up off the ground a little water rinse and eat away. Also is there a better diet for different races or ethic backgrounds one that evolved with that culture.

I’m switching career fields and going into medicine. I find this project truly fascinating and can’t wait to learn more about the intersection of ecology and healthcare found in the foods we eat and the microbes we harbor. Thank you for all your hard work and sharing your research with us Jeff!

I like your writing style and your sense of adventure (gutventures). Interesting to see how gut flora dramatically change based on diet in the graphed results of your Self-Survey method. My gut gets out of whack once in awhile and I whack it back into line with some capsuled probiotics for a few days. This is not backed up by any back-end science (i.e. stool sampling), but I think it works. However recently I read that the stated strength of probiotics is all over the map, i.e. sometimes BS, but as you pointed out a few billion sounds good but doesn’t make much of a dent compared to the population numbers where it’s headed. To get to the meat of my missive though is a recent Self experiment which is related to the idea that modern highly cross-bred wheat is a problem for the older hunter-gatherer digestive system – no, not the cult of anti-gluten but just the complex modern wheat protein. I have found that I get mild but persistent skin rashes from eating too much wheat being mostly the whole grain version, which is an intolerance symptom. Recently though I was wacking my system again but this time using Bio-K, a made in Canada liquid fermented probiotic (requiring refrigeration) containing “L Acidophilus + L Casei” bacteria. To my surprise, my mild itchy skin rash disappeared for about a month with no change in my diet after just a few days of consuming said product. My assumption is that this temporary change in symptoms was due to the bacteria processing the wheat protein differently – i.e. I could now digest it, as a skin rash is often the body trying to get rid of food that could not be fully processed. Not an intentional experiment, but a real change in my “health” due clearly only to different bacteria in my system. No other probiotic I’ve used has had this effect. I’m signed up for your book, and look forward to reading it. I think this area of investigation is one of the top key health research fields of the 21st Century – just a gut instinct. :o)

I didn’t see any mention of the Weston A Price diet which is basedon traditional cooking styles, including fermented foods. I hope you have heard of it, because it is right up your alley. Another interesting book I have been reading recently that addresses these issues is Bill Mollison’s fermentation and human nutrition. Fabulous focus on gut biomes, even though it was written decades ago.
Seth P

I have stopped smoking and am bloated with large weight gain on the tummy area only. Apparently when you stop smoking proteobacteria and bacteroidetes increase at the expense of firmicutes and actinobacteria. I do not understand mich of this despite extensive reading. How would I redress this imbalance and change it back to higher firmicutes and so. K

But we probably have to wait yet another year after that for you to publish your book. I promise to buy it even if you give us some heads up info in the meantime. Some of us are struggling to maintain our health in the midst of all kinds of conflicting diet information. One big issue with this whole study is that we don’t know what kind of body you have. We don’t all metabolize the same. Are you going to do 23andme? And again – I am very grateful for your work on this and can’t wait to get more information. I’ve actually been worried about you since the poop transplant – there was only one post since and that was quite a while ago.

Hi Jeff,
I am very fascinated by your bio hacking experiments. The only thing that I have found surprising is that I expected here back to IDT’ The only thing that I have found surprising is that I expected here bacteroidetes to be the dominant bacteria in your high fiber diet and the firmicutes to be in the minority. This is based on the work of Brenda Watson’s research and book The Skinny Gut Diet.
My understanding, according to Miss Watson and others in the field is that high bactrousered to firmicutes is the typical ratio found in high fiber diet and in those of lien mice and human beings. I would appreciate your thoughts on this. also, I was wondering where you posted the rest of your experiment of one results.

What I find amazing is a lot of people do well on very meat based diets and a lot do well on plant based diets. It seems high carb high fat is the problem. You can have only one or the other. Diet is very confusing.

Are you a sulfide-gas producer? According to gg.gg/D-Piger , about half of us are. If you agree with those who consider hydrogen sulfide harmful to the colon, the way to reduce it is by eating less high sulfur foods and keeping the colon acidic with fermentable carbohydrates.

You could test what a low sulfur diet does to your microbiome, but if you don’t have sulfide-producing bacteria to begin with, it might not be particularly beneficial for you.

GREAT article. I am quite confused by the Firmicutes & Bacteroidetes, & I’m hoping you can help me understand. I have read about both before & I had thought that it was the Bacteroidetes that enjoyed fermenting fiber. So I looked up many references & this is just one example of what I found: “. . . Moreover, when the diet is high in fat, the obesity-friendly firmicutes increase (the exception being a ketogenic diet), yet a high-fiber diet helps bacteroidetes increase. In addition, researchers observed that overgrowth of firmicutes led to chronic systemic inflammation . . . .”

Yet, in your case, you seem to be saying that you believe the Firmicutes were the bacteria happily fermenting your high fiber NewOrleans diet, right? And the Bacteroidetes took over when there was much less fiber to ferment (your desert diet). I know that I now must read ALL that you have written, but I’m hoping you can “unconfuse” me soon, so I can better grasp the rest of your journey!

note the firmicutes argument for obesity doesn’t hold up at the population level – in the american gut data – and other studies – people fall along a spectrum… note the hadza – who are thin – are dominated by firmicutes….. note also when you see higher levels of bacteroidetes in some rural populations, it’s due to an increased abundance in the genus prevotella – which is driven by whole grain consumption. remove the whole grains, and the prevotella drops and thus the bacteroidetes…

I was wondering what kind of plant fiber you were eating on your high fiber + meat diet? Were these typical veggies? Lots of onions? Starchy veggies or root veggies? Any grains?

I’m just wondering if any fiber works to get the effect you had and when people talk about soluble fiber are they talking regular veggies like carrots and broccoli or including root veggies or grains?

Thanks, it would help a lot

I have eczema/food allergies since I was young and since clostrida was shown to eliminate peanut allergies (in mice) and clostridia is part of the firmicutes I figure trying to boost firmicutes is a good start.